File importing problem and problem with "MSnbase readMSData" tool

Workflow4Metabolomics
1

Hello.
Since this morning I have two problems. On the one hand, I'm having trouble importing mzXML files and even TSV files (they remain grey in the history with no change) and on the other hand, when I manage to import them and launch the workflow, the “MSnbase readMSData” tool gives output files with 0 bytes, which blocks the next steps.
I've tried deleting everything and starting again, but it always does the same thing.

Thanks for your help.

Antoine

2

Hi, that sounds more like a server issue than a tool issue. Is there any text in the standard input or output from those tools?

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3

Hello, Galaxy seems to have some problems, as you mention, everything stay "grey". I face the same problem on my side. Hopefully it won't last long !

4

Yes I think it's more a server issue. I haven't had any change since yesterday. I hope this problem will be solved soon.

5

Problems also with statistical tools

6

This problem is shared by everybody I would say.

Globally, it seems the jobs are now run without issue (explaining the green status), but somehow it is not possible to retreive the data obtained. For example, you may have information about the number of lines and columns of a tabular file obtained as output (meaning the job ran and finished with your results ok), but no display of the content through the "eye" button, and an empty file when trying to download it. And you also get red if you try to use these datasets as input of other jobs, as it will find an empty file also. So at some point the content of the datasets just got lost after the analysis ended, even though it existed at some point (since the metadata about lines/columns do exist).

There are other tickets with the same issue (like this, this and this). Part of these tickets are currently taken in charge by someone from @team.galaxy so we will wait for now.

Best regards,
Mélanie

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7

Hello,

We’ve just applied a temporary patch and have received positive feedback so far.
Could you please test it on your side as well and let us know if the issue is resolved for you too?

Thomas

8

Hello,
The jobs seem to be going better on my side, the MSnbase outputs are not empty.
Thank you !

9

Hi,
I confirmed yesterday some jobs I launched worked. But since, my new jobs stay in grey. Is it related to the same problem or it is a new one ?
Binta

10

Hi,
I have the same problem, my jobs stay in gray during the retcor step. I got an answer here
Antoine

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